Is Specimen Days a novel, or three novellas loosely threaded together? This is just one of the many genre disputes in which this book can become ensnared. The opening story tackles historical fiction, the second takes on the detective thriller genre, the third is science fiction. To many critics in Cunningham's native America, this represents a three-stage journey from the sublime to the ridiculous. "Science fiction will never be Literature with a capital L," the New York Times has loftily declared (apropos of Margaret Atwood's Oryx and Crake), and Specimen Days is encountering similar flak.

"In the Machine", the most uncontroversially "literary" of the three tales, is set in 19th-century New York, and features Lucas, a 12-year-old boy caught up in the merciless grind of the industrial revolution. Slaving at the factory that claimed the life of his brother Simon, he becomes convinced that machines are inhabited by ghosts who lure the living into them. His desperate attempts to warn Catherine, Simon's bereaved fiancée, of her impending fate, are hampered by an inexplicable compulsion to spout Walt Whitman's verse.

"The Children's Crusade" takes place in post-9/11 Manhattan, where Cat, a hardboiled police psychologist who deals with cranks and wannabe assassins, is horrified to discover a secret "family" of pre-teen suicide-bombers. The children blow up their victims at random, using Whitman's Leaves of Grass as their rationale. When Cat bonds with a 12-year-old bomber who reminds her of her own lost son, Luke, her shallow relationship with futures trader Simon is undermined by yearnings for a pre-industrial utopia.

"Like Beauty" takes place in a post-nuclear future, when New York has been turned into a tawdry theme park. Simon, an android whose programming makes him recite Whitman whenever he's in danger of feeling human emotion, goes on the run with Catareen, a reptilian alien. Teamed up with Luke, a 12-year-old street kid, they are finally offered escape to a paradisal new planet, but Simon risks losing his place in the spaceship to stay with the woman - or lizard - he loves.

Summarised thus, the stories may seem unpromising, even silly, but Cunningham is a superb writer and Specimen Days is full of the same lovely prose and generous spirit that distinguished his previous novels. Here he is describing a nocturnal taxi ride: "Only at these subdued moments could you truly comprehend that this glittering, blighted city was part of a slumbering continent; a vastness where headlights answered the constellations; a fertile black roll of field and woods dotted by the arctic brightness of gas stations and all-night diners, town after shuttered town strung with streetlights, sparsely attended by the members of the night shifts, the wanderers who scavenged in the dark, the insomniacs with their reading lights, the mothers trying to console colicky babies, the waitresses and gas-pump guys, the bakers and the lunatics." Such evocations of the human continuum - Whitmanesque in their scope, but pure Cunningham in their melancholy delicacy - recur throughout.

In truth, the territory here, stripped of its genre trappings, is the same as in The Hours or A House at the End of the World. In those novels, as in these stories, preternaturally self-knowing and articulate characters are grieved by life's unaccountable refusal to measure up to ideals. Held back by their attachment to family, friends and lovers, they stare longingly at the infinite beyond, painfully aware that what they really need is the ability to inhabit the present moment. The lizard-woman Catareen calls this elusive state of grace "stroth", but it's what all of Cunningham's characters, including his celebrated reinvention of Virginia Woolf, are seeking.

Indeed, it may be Cunningham's awareness of his work's philosophical predictability that drove him to such a daring revamp of his narrative exteriors. If the principal thematic tension is not negotiable, then a high-speed car chase through the futuristic ruins of New Jersey may be just the thing to keep ennui at bay. Impressively, though, there's palpable authorial enthusiasm behind most of these added thrills. Cunningham is to be applauded for exploring alternatives to a comfy literary franchise.

Granted, Specimen Days declines in quality as it goes along. "In the Machine" is a pitch-perfect fusion of gothic melodrama, psychological realism and the mysterious spark that enlivens unforced visions. "The Children's Crusade" builds to a potent ending, but its marriage of profound compassion and cop-show clichés is unstable. "Like Beauty" handles Catareen's alienness with marvellous empathy but is bogged down by the usual demerits of mainstream science fiction: creaky expository monologues about how the future came to be, cringe-making references to people taking a "dermaslough" or hydraulicking their pods, and worship of concepts at the expense of narrative credibility. The wisecracking Luke seems derived from a Hollywood buddy movie, reciting impossibly adult repartee, and the somewhat kitsch finale fails to do justice to the book's overarching ambition.

And yet, while reading "Like Beauty" I was conscious that, had I read it in a sci-fi anthology when I was 15, I would have been awestruck by it, moved beyond tears, changed for ever. Today, I'm sufficiently sophisticated to notice the author wrestling with his material, struggling to beat it into a shape that looks natural, straining to make its hokeyness transcendent. If the aim of reading good books is to be transported, it would be better if we never developed this jaundiced analytical eye, but sadly we do. And perhaps the fiction Cunningham is attempting here is pitched at a reader who doesn't exist: an adolescent who can leap straight from Star Wars to Henry James, or an adult steeped in Woolf and Whitman who nevertheless retains a childlike capacity to be moved by X-Men 2

Even so, I heartily recommend volunteering, just for a few hours, to be that non-existent reader. Specimen Days, in among its misfires and misjudgments, contains more incidental beauty and emotional insight than many impeccably dull items on the shortlists of prestigious literary prizes. And it's by far the best gothic historical sci-fi cop thriller you'll ever read. Michel Faber's new short story collection, The Fahrenheit Twins, will be published by Canongate in September. · To order Specimen Days for £13.99 with free UK p&p call Guardian book service on 0870 836 0875.